[Biopython-dev] [Biopython (old issues only) - Bug #3430] (Resolved) Error parsing PubMedCentral XML files

[redmine at redmine.open-bio.org]

Issue #3430 has been updated by Travis Wrightsman.

Status changed from New to Resolved
% Done changed from 0 to 100

NXML file was improperly formatted.

----------------------------------------
Bug #3430: Error parsing PubMedCentral XML files
https://redmine.open-bio.org/issues/3430#change-15300

* Author: Paulo Nuin
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 
* URL: 
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It seems that there is an error parsing locally downloaded PubMedCentral xml (extension nxml) files. Using the code 

@
from Bio import Entrez
handle = open('nihms83342.nxml')
records = Entrez.parse(handle)
for record in records:
    print record
@

the following error occurs (copied from iPython), even though the XML header contains the declaration


---------------------------------------------------------------------------
NotXMLError                               Traceback (most recent call last)
<ipython-input-5-e78d8d3c3888> in <module>()
      2 handle = open('nihms83342.nxml')
      3 records = Entrez.parse(handle)
----> 4 for record in records:
      5     print record

/Library/Python/2.7/site-packages/Bio/Entrez/Parser.pyc in parse(self, handle)
    229                         # We did not see the initial <!xml declaration, so
    230                         # probably the input data is not in XML format.
--> 231                         raise NotXMLError("XML declaration not found")
    232                 self.parser.Parse("", True)
    233                 self.parser = None

NotXMLError: Failed to parse the XML data (XML declaration not found). Please make sure that the input data are in XML format.

The XML file in question is attached.

---Files--------------------------------
nihms83342.nxml (74.9 KB)


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